Monthly Archives: March 2014

Hi there folks! After a long time absent I finally gathered enough willpower and decent topic material to post something in this humble site of ours. In this article I’ll talk about a relatively recent technology that is quickly growing and can revolutionize the way we study fossils and other biological subjects, as well as the way we can help humanity in an applicable way.

But first, some shameless advertising because it’s always good to spread this kind of thing around: if you missed Bill Nye’s debate against that other guy you can watch it in its entirety clicking here. Regardless of whether you believe Bill inadvertently helped the Creation Museum go ahead in building its replica of Noah’s Ark (until they run out of money again, that is) or not, it’s still a great source of entertainment to watch and show your kids, teaching them the difference between spouting nonsense that vaguely sounds convincing to actual debating using facts and that’s okay to not know something rather than pretending you know all. Second but not less important, Cosmos: an Space Time Odyssey episodes are available online by clicking here. As of now I myself couldn’t watch because my internet lets me down, but for those who missed it or don’t live where it’s airing, go ahead and watch it for your brain’s content.

Now for my topic properly, the astounding technology in question is 3D printing. If you’re unfamiliar with 3D printing: it’s the process to which a tridimensional model made in a computer is transformed into a physical object by means of a machine – the 3D printer – that will sculpt the desired object. In 3D. I first came to know of this technology sometime during 2006; it was during the development of Spore, and Maxis considered offering a service to which players could import their creations and receive it as physical miniature, and it did come live two years later when the game was released. It had some limitations such as not being able to reproduce overly thin features and a very grainy texture thanks to the material used, which also made the model incredibly fragile. Since then 3D printing became more refined and widespread. Nowadays there are several online services to which you can order your very own 3D models such as Shapeways, i.Materialise, Sculpteo and so on, and make them in better details and made of more durable materials than before.

Yup, EBA is out of business.

Apart from the alluring prospect of printing your favorite video game characters and prototyping for engineers (my priorities are set right), 3D printing also offer some interesting possibilities when it come to the study and teaching of biology – specially paleontology – and the development of prosthetics. For instance, regarding the former, it can help paleontologists in the extraction of fossils. As of now, the process to which fossils are dug up and prepared to be analyzed properly in a lab is something along the lines of:

Find fossil bed -> very carefully excavate the site -> find fossil embedded in rock -> very carefully excavate fossil -> shed tears as you accidently damage the fossil while excavating -> wrap fossil in plaster and ship it to the lab and hope it arrives safely -> receive fossil in lab -> very carefully remove plaster not to damage fossil -> shed tears as you accidently damage fossil while removing plaster with saw-> further shed tears as you accidently damage the fossil during analysis.

Pictured: shed tears.

For the reasons above, it’s understandable that methods that allow studying these fossils while minimizing risks are very welcome. One such method that quickly gained notoriety was the use of CT scans, which generated 3D models of the specimens to which scientists could peek at their inner structures without actually cracking open the fossil. It was by this very technique we came to know that Pachycephalosaurus had a sturdier helmeted skull than previously thought, making the old assumption that they butted heads just a little bit more plausible. While this was an amazing step forward in the study of fossils, the next step came soon after; this technique was mostly used on fossils already cleaned up of sediments, but the same method proved to be just as effective to fossils still encased in rock slabs.

Some paleontologists were afraid that excavating the rock would damage the skeletons they work so hard to retrieve. As a solution, they simply extracted the rock around with the fossil inside, scanned it thus generating a 3D model like its predecessor, and then printed it. The result was a near perfect replica of what was encased in the rock. I can’t stress enough of how amazing this is: the remains of a creature, extinct for millions and millions of years, reproduced as if removed from its mineral tomb for everyone to look and touch.

In this case, shed tears of joy.

All seems to be favorable evidence that printing fossils might become an even bigger part of paleontology in the future. While I personally don’t believe this process would come to replace the usual method of digging up fossils entirely, as foreshadowed by the nameless paleontologist in Grant’s team in Jurassic Park, – in fact, even if the 3D print is a perfect replica, it still doesn’t beat the real thing – I do believe that employing this technique would minimize the risks of damaging specimens; the fossils would still need to be removed from their locations lest they continue to erode and be affected by earthquakes, rains and whatnot as was the case of the forelimbs of the baby Chasmosaurus unearthed just a few months ago in Canada, which could have been further damaged had it not been removed. Not only it would help knowing exactly where paleontologists should remove the sediments if they judge it to be necessary, the 3D model generated could help in both having a bigger picture of the creature they’re dealing with, as in arranging the pieces to form a posture if the animal was alive (assuming that it’s possible for them to fit in the machines), as well as aiding museums show said findings to the public.

The process to which fossil replicas are made for museum exhibitions is just as risky and labor intensive as the digging of fossils: a team of artisans is employed to make castings out of the original fossils – very carefully not to shed tears as they accidently damage the fossil in the process- and once ready probably months later the skeleton is assembled and put to the public’s delight. The problem is, because of its complexity and requirement for skilled workmanship to achieve maximum quality, these replicas are hard to come by, and so the museums that get to expose them take extra care that they’re not damaged, in the form of a polite sign asking visitors not to touch it when in reality they really want to punch whoever break them in the face. The problem of interchangeability is minimized if the museum makes more replicas intended to other museums, as it was the case of the dodo skeleton offered by the Royal Ontario Museum.

Say “thanks, Royal Ontario Museum”.

While the dodo skeleton was a very nice gesture for other museums, it is a rather small specimen. It’s one thing to make a replica of a bird’s skeleton and ship it to other museums while still providing an affordable price. It’s quite another trying to do the same with a huge dinosaur skeleton like an 85 feet long Brachiosaurus. But imagine if museums could print these skeletons, regardless of their size and complexity. I don’t want to be mean to the people in the trade of fossil replicas, but the idea that a museum could print their own skeletons to their exhibitions using the skeleton models created by MRI scanning is a fascinating one, and advantageous not only to the museum but those who study in it. It’s not something still in the realm of imagination: there is already the employment of 3D printing to reproduce animal’s skeletons for educational purposes (as well as other areas, but we are a biology-centered blog), so plans to make an actual exhibition out of entirely 3D printed specimens seems to me to be just as far out in the future as the use of 3D printed skeletons in biology classrooms that give students a more tangible and interactive tool for learning.

Another interesting use of 3D printing in the field of biology is its medical use. Somewhere in the world someone thought that using polymers and metal to make miniatures was too mundane, and skin tissue was a better material. Whatever the case is that brought about the use of this technology in the medical area, 3D printing functional organs seems to be a new reality, and anything from functional ears, hearts, livers, even eyes are being worked on to aid patients in need of transplants or face reconstructions. More recently, only few days ago, a woman successfully got a 3D printed skull replacement.

I don’t want to post a picture of that here, so have a picture of Gummy instead.

So while more complex organs are still on their developmental phase, there’s this immediate use where 3D print can be used to replace bone structures, even prosthetic limbs. In order words, not only 3D printing opens ups possibilities to print miniatures of your favorite Pokémon and learn about prehistory, it also gives a bright future to those struggling in the line of organ donations. Instead of waiting in line, medics could simply print a new organ.

I just want to finish this post by saying that this is what I find most fascinating about technological advancement: you start out with a simple tool with maybe one or two uses, and then people will create new forms of this tool, for uses one couldn’t possibly imagine. Something that started as a printer that didn’t use paper came to be the door to many other wonderful developments. The downsides of the modern 3D printers regarding their price, operation and general availability are really only temporary.

Well then, I hope you have enjoyed my blabbering article and, as usual, comments and questions are appreciated!

This is the first bird featured in Friday Fellow and I have chosen it for a special reason: it’s binomial name is Tyrannus melancholicus, the melancholic tyrant. Isn’t it almost poetic?

Found from southern United States to the northern half of Argentina, the Tropical Kingbird, known as sirirí or suiriri in Spanish and Portuguese, is very well adapted to human disturbed areas, so it is easily spotted along roads or at gardens and parks. Populations inhabiting areas of great seasonality usually migrate to warmer areas, mainly towards southern United States during the winter in the southern hemisphere.

Tropical Kingbirds are mainly predators, capturing insects intercepted in flight. They don’t seem to be very sensitive to chemical defenses of butterflies, eating even some unpalatable ones and species with similar color patterns, though some species highly unpalatable are indeed rejected. Ocasionally they may also eat fruits.

During the breeding season, they form couples and build together a bowl-shaped nest using small branches, straw and nylon and plastic threads. The female usually lays three eggs in the nest and both birds incubate them and take care of the chicks.

As a consequenceof its adaptability to humans, it is not endangered at all, at least until now, and has a status of Least Concern (LC) by IUCN.

I have already written on the problems of taxonomy in small and not-so-cute groups in a previous post, where I talked about the fact that several species, after being described, are completely ignored for decades or centuries. Here I will focus on the other extreme: the species yet to be described.

This is not a very big problem in very well studied groups, such as vertebrates and flowering plants, but less attractive groups, like worms, suffer a lot by the lack of taxonomists. I am going to use land planarians as an example, again, since it is the group that I work with.

Land planarians have been shown to be important predators of invertebrates in forests, as well as good indicators about the degree of disturbance in those ecosystems, but most species are still unknown. Only in Brazil, more than a hundred species have been described only for the Atlantic Rainforest and possibly at least an equal number is yet unknown. The situation is even worse in other regions of the country or neighbouring countries, where there are almost no species described at all.

Despite this small knowledge of the group, eventually some works regarding community structure are published, where a list of land planarians from the study site is presented. Let’s take a look at some of those lists:

1. Species of land planarians in four different habitats of the National Forest of São Francisco de Paula, southern Brazil. In Carbayo et al., 2001:

There are 28 distinguished species, but only one identified (Geoplana ladislavii), one not sure (Geoplana pavani) and two with the same name, but refering to different species (Notogynaphallia marginata). The others were yet unknown.

2. Species of land planarians in four different habitats of the National Forest of São Francisco de Paula, southern Brazil. In Carbayo et al., 2002:

A similar table, in the same area, by the same authors, about one year later. We can see 3 new species in the study: Geoplana franciscana, Geoplana josefi and Notogynaphallia guaiana, which were described in 2001. They were probably among the species listed in the first study, but which of them? Was Geoplana franciscana the species assigned as Geoplana sp.1, Geoplana sp.2, Geoplana sp.3…?

3. Abundance of species of land planarians in Araucaria Forest of the National Forest of São Francisco de Paula, southern Brazil. In Antunes et al., 2012.

The same area again, 10 years later. We can see that there are more species already described, but many more still awaiting a name.

When we consider a single study about ecological communities by itself, the fact that the species found are not named is not such a big deal, since the main purpose is to measure patterns of abundance, richness and diversity and the interaction of biotic and abiotic factors on the communities. However, when comparing studies, the unidentified species become simply useless data. How can you be certain about what Geoplana sp.5 is in each study?

We urgently need more taxonomists working on those less prestigious groups, so that our ecological studies may have a wider role in conservation and understanding of nature.

This palm, which belong to the species Ceroxylon quindiuense, is the national tree of Colombia and native to the Cocora Valley, a high altitude valley of the Andean region in the department of Quindío, Colombia, from where it was considered basically endemic. However, recently a significant population was found southwards in the Andes of northern Peru.

Ceroxylon quindiuense in the Cocora Valley, Quindío, Colombia. Photo by Diego Torquemada*. Taken from commons.wikimedia.org

As all species in the genus Ceroxylon (“wax wood” in Greek), the Quindio wax palm has a cylindrical trunk covered with a white wax marked by scars left by leafbases. It is also the tallest palm in the world, reaching as far as 60 m in height or even more.

Until the beginning of the 20th century, it was a very abundant species in Colombia, but its population was already being reduced due to several activities, mainly by harvesting it as an important source for manufacturing candles during the 19th century. Also, until very recently young leaves were cut to be used for Palm Sunday, leading to death or delay in growth. Nowadays both practices are highly reduced, but the species is still threatened by other activities. The raising of cattle have turned most of the forest where the Quindio wax palm grows in pasture and, despite the large amount of trees growing in the pasture, there are no young individuals, since all (or almost all) seedlings are eaten by cattle. Thus, it is considered Endangered (EN) in the Plant Red List of Colombia and Vulnerable (VU) by IUCN. As an initiative to save the species, it is legally protected in Colombia since 1985, when it became the national tree of the country.

The reduction of the populations of wax palm also threatens species associated to them, like the yellow-eared parrot, which nests in the hollow trunks of wax palms and is an endangered species according to IUCN. But that’s another fellow…

The 18th and 19th centuries were well marked by great worldwide expeditions by naturalists aboard ships travelling all around the world. Charles Darwin is certainly the most famous of them, but he was not the only one.

One of those naturalists was Karl Ludwig Schmarda, born in 1819. He studied in Vienna and was later a professor at the University of Graz, Austria. From 1853 to 1857, he travelled around the world investigating several locations and collecting primarily invertebrates. After his return, he published a work entitled Neue wirbellose Thiere beobachtet und gesammelt auf einer Reise um die Erde 1853 bis 1857 (New invertebrate animals observed and sampled on a travel around the Earth, 1853 to 1857).

Among the countless animals that he described, there was a worm which he called Prostheceraeus terricola. The description is as it follows:

The body is less flat than in other planarians, elongated, behind pointed and lanceolate, front almost transversally cut. The feelers are short and awl-like pointed. The back is strongly convex, almost grass green with a purple line running fully along it. Margin not wave-like and purple-colored. The ventral surface is greenish gray. Length 20mm, largest width 5mm. The eyes are at the inner border and the base of the feelers. The group at the neck I didn’t observed. The mouth opening is in the front third. The sexual opening I did not found.
The reason of my incomplete knowledge of this animal form is due to the circumstance of finding only one specimen in the top part of the Quindiu passage above the region of the mountain palms, which I sketched it in Gallego, since it was already deteriorating, to undergo a revision back at the station in Tocho.

Here you can see the drawing of the animal:

Drawing of Prostheceraeus terricola by Schmarda, 1859

Schmarda put other worms in the same genus, all of them marine. The genus is valid until today for marine species and they are classified as belonging to the Polycladida, those beautiful sea flatworms.

In fact, this animal actually looks kind of similar to a polyclad, but Schmarda found it on the top of the mountains! Quite unusual, and unfortunately he found only one single specimen.

Prostheceraeus giesbrechtii, another species described by Schmarda (1859). Photo by Parent Géry taken from commons.wikimedia.org

Later, in 1862, K. M. Diesing made a revision of turbellarians and defined that, as the creature lived on land, it was certainly something other than a polyclad and changed it to a new genus which he called Leimacopsis (slug-like):

As you can see, it’s again simply a repetition of Schmarda’s description based on that single specimen from 20 years earlier, but from Diesing on, the animal started to be considered a land planarian rather than a polyclad.

Now in 1899, Ludwig von Graff published his great monography about turbellarians and I’m certain that I saw something about Leimacopsis there. Unfortunately I never found a digital copy of it and I don’t have a physical copy easily accessible either, but according to Ogren (1992), it has only a repetition of Schmarda’s account. Graff, however, changed the spelling to Limacopsis, but this is not valid according to the International Code of Zoological Nomenclature.

In 1914, finally a new article, by O. Fuhrmann, was published with information about land planarians from Colombia. He begins commenting that there were only three species known for the country by that time, one of them being Limacopsis [sic] terricola. However, the species was not found again this time…

The years passed and nothing changed. In 1991, Ogren and Kawakatsu, in part of their index to the species of land planarians, comment that several researchers, like E. M. Froehlich and L. H. Hyman, considered Leimacopsis terricola as possibly being a slug.

In 1992, Robert Ogren wrote an excellent revision of this species, which presents all information I have given here and much more. He concluded that the organism is a species inquerenda (needing further investigation) and nomen dubium (doubtful name). It is not possible to assign the animal as either a flatworm or a mollusk, or anything else due to the lack of information. Ogren considered it as “clearly part of the lore of Cryptozoology”.

As we can see, cryptids don’t need to be big animals like dinosaurs or big feet. Even a small slug-like worm from the Andes may fit.

Leimacopsis terricola is certainly an interesting organism. What was it really? Was it real? Maybe an extensive research in the area would reveal something… or not. Let’s wait and hope… Or perhaps… what about going to an adventure in Colombia’s Andean region in search of the mysterious creature?

Moseley, H. 1874. On the Anatomy and Histology of the Land-Planarians of Ceylon, with Some Account of Their Habits, and a Description of Two New Species, and with Notes on the Anatomy of Some European Aquatic Species. Philosophical Transactions of the Royal Society of London, 164, 105-171 DOI: 10.1098/rstl.1874.0005